AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -irpoE_pyro_opreg_300.orf -g0.419 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.419 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 PH1408 233 226aa long hypothetical protein #2 PH1409 250 721aa long hypothetical protein #3 PH1410 117 332aa long hypothetical dipeptide transport system permease protein dppB #4 PH1414 26 129aa long hypothetical protein #5 PH1415 93 343aa long hypothetical 5' nuclease Motif number 1 ATTTCATAGGCGTACATCTCTCTTTCCTCGAG 1 42 0 CGTACCTCTC 0.946173 -192 TAATATATCCTCTTCCCCTTTCTATATGCCTC 1 156 0 TCTTCCTTTC 0.993814 -78 CAATAAGCCTTCTACCTCTCTCAGTCAGCTTG 1 188 0 TCTACCTCTC 0.989394 -46 ATAATTTGGATCTTCTATTTTCCACAAAGTGA 2 157 1 TCTTCTTTTC 0.973506 -94 TAATCTTTCTTCTCTCTTTTCTTTAT 3 5 1 CTTTCCTCTC 0.970057 -113 ATATCCTCTTCTTTTTTCAATTTTTG 4 7 1 TCTTCTTTTC 0.973506 -20 TGATGATGAACCTTCCCCTCACCTGAAAGGTG 5 41 1 CCTTCCTCAC 0.978147 -53 ACCGGTGTGCTCATCACCTTTCAGGTGAGGGG 5 55 0 TCATCCTTTC 0.966432 -39 ***** ***** Masking position 9 Map Score: 9.69503 Number of sites scoring better than the average of aligned sites = 386 Number in coding regions = 352 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 2 AAAGGGGAAGAGGATATATTACAAGCTGACTGAGA 1 167 1 AGTAAACAAG 0.977735 -67 CCCTCTACTCAAGATTTTCAATAAGCCTTCTACCT 1 203 0 AGTTTATAAG 0.872008 -31 AGCATCTTCAAGGTGAAACAATAAGC 2 2 0 AGGAAATAAG 0.977762 -249 CACCTTGAAGATGCTTAAAAATCAGTGGTGTATCA 2 22 1 AGTTAATCAG 0.980794 -229 ATGTTTTTGAATGTTTTATGATCAAAATGATACAC 2 49 0 AGTTAATCAA 0.861403 -202 AGGTTATCCAAAGAGATATAACCAGGCACCTCGCT 2 210 0 AGGAAACCAG 0.978996 -41 ATTTTTATTTATGCGATAATATAATTCTCAAACGA 3 58 1 AGGAAATAAT 0.830758 -60 TTCTCAAACGATGTTATAGAACAAGAATGTACAAG 3 82 1 AGTAAACAAG 0.97773 -36 AGGTGAGGGGAAGGTTCATCATCAGACTTGATATC 5 30 0 AGTTAATCAG 0.982301 -64 * * ** * ***** Masking position 11 Map Score: 8.27317 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 103 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 GCTTATTGTTTCACCTTGAAGATGCT 2 7 1 TGTTTCACCT 0.986244 -244 AAATCAGTGGTGTATCATTTTGATCATAAA 2 40 1 TGTATCATTT 0.892607 -211 TTTTTTGAGATGTTTAACCTAGTGTAAATG 2 100 1 TGTTTAACCT 0.956901 -151 TGTTATAATTTGGATCTTCTATTTTCCACA 2 153 1 TGGATCTTCT 0.905081 -98 TTTTCGATCTTGGTTCACTTTGTGGAAAAT 2 173 0 TGGTTCACTT 0.97466 -78 TATATCTCTTTGGATAACCTTCCCTGGTGA 2 225 1 TGGATAACCT 0.953348 -26 ********** Masking position 5 Map Score: 4.11655 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 143 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 ATATAGAAAGGGGAAGAGGATATATTACAAG 1 161 1 GGGAGAGGAT 0.988593 -73 TGACTGAGAGAGGTAGAAGGCTTATTGAAAA 1 193 1 AGGAGAAGGC 0.956678 -41 TGAAAATCTTGAGTAGAGGGTGGTGA 1 218 1 GAGAGAGGGT 0.993299 -16 ACTTTGTGGAAAATAGAAGATCCAAATTATA 2 156 0 AAAAGAAGAT 0.788692 -95 AAATTGAAAAAAGAAGAGGATAT 4 3 0 AAGAGAGGAT 0.983452 -24 CCTTTCAGGTGAGGGGAAGGTTCATCATCAG 5 40 0 GAGGGAAGGT 0.963292 -54 GCACACCGGTAGGCTGAGGGTGATAAT 5 77 1 AGGTGAGGGT 0.97338 -17 *** ******* Masking position 7 Map Score: 4.96649 Number of sites scoring better than the average of aligned sites = 506 Number in coding regions = 472 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 TAAGCTTGAGATTCTTAAAATCCTCGAGGA 1 20 1 ATTCTTAAAA 0.969081 -214 CACCTTGAAGATGCTTAAAAATCAGTGGTG 2 22 1 ATGCTTAAAA 0.948422 -229 TTTATTACTAATTGTTATAATTTGGATCTT 2 141 1 ATTGTTATAA 0.969086 -110 ATTGTTATAAACTTTCAGAG 5 1 1 ATTGTTATAA 0.969086 -93 ********** Masking position 5 Map Score: 1.40671 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 34 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 TCATCAGCATATAAAGGAATTACAAGAGTTAGGC 1 113 1 ATAAGGATAA 0.992981 -121 GTTAGGCCTCATAAAGGAGGCATATAGAAAGGGG 1 140 1 ATAAGGGCAA 0.979869 -94 ATCTCAAAAAATAAGGGAATTAGAGAGATGTTTT 2 77 0 ATAAGGATAA 0.992981 -174 TGGTGTTTAAATAAGGGCAATAAAGAAAAGAGAG 3 22 0 ATAAGGATAA 0.992965 -96 **** ** * ** * Masking position 4 Map Score: 0.604424 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 15 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 ********** No masking Map Score: 1.40931e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ACATCTCTCTTTCCTCGAGGATTTTAAGAATC 1 29 0 TTCCTCGGAT 0.704778 -205 TTCTATATGCCTCCTTTATGAGGCCTAACTCT 1 137 0 CTCCTTTGAG 0.913909 -97 CTTATTGTTTCACCTTGAAGATGCTTAAAAAT 2 12 1 CACCTTGGAT 0.993438 -239 GATCTTGGTTCACTTTGTGGAAAATAGAAGAT 2 166 0 CACTTTGGAA 0.781162 -85 TATAACCAGGCACCTCGCTAATAAGCTTTTCG 2 197 0 CACCTCGAAT 0.918876 -54 TTGGATAACCTTCCCTGGTGATGTAAG 2 234 1 TTCCCTGGAT 0.903445 -17 ATTTGCCCCTCCTTGTACATTCTTGTTCTA 3 98 0 CTCCTTGCAT 0.967367 -20 GTGTGCTCATCACCTTTCAGGTGAGGGGAAGG 5 51 0 CACCTTTGGT 0.903553 -43 ******* *** Masking position 3 Map Score: 1.21201 Number of sites scoring better than the average of aligned sites = 473 Number in coding regions = 445 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 ********** No masking Map Score: 1.40931e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 10 ********** No masking Map Score: 1.40931e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 11 ********** No masking Map Score: 1.40931e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0